Regulation dynamics of WGD genes during yeast metabolic oscillation

Molecular Biology and Evolution

Volumn 25, Issue 12, 2008, Pages 2513-2516

  Chen, Hong ^a   Xu, Lin ^a   Gu, Zhenglong ^a  

^a Department of Obstetrics Gynecology

Author keywords

Metabolic cycling genes; WGD; WGD fermentation hypothesis; Yeast

Indexed keywords

ARTICLE; FUNGAL GENE; FUNGAL GENETICS; FUNGAL METABOLISM; GENE CONTROL; GENE DUPLICATION; GENE EXPRESSION; METABOLIC REGULATION; NONHUMAN; SACCHAROMYCES CEREVISIAE;

FERMENTATION; GENE DUPLICATION; GENOME, FUNGAL; OXYGEN; SACCHAROMYCES CEREVISIAE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 56449106910     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn212     Document Type: Article

References (29)

1. Blank LM, Lehmbeck F, Sauer U. 2005. Metabolic-flux and network analysis of fourteen hemiascomycetous yeasts. FEMS Yeast Res. 5:545-558.
2. Blomme T, Vandepoele K, De Bodt S, Simillion C, Maere S, Van de Peer Y. 2006. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7:R43.
3. Byrne KP, Wolfe KH. 2005. The yeast gene order browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15:1456-1461.
4. Conant GC, Wolfe KH. 2007. Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol Syst Biol. 3:129.
5. Davis JC, Petrov DA. 2005. Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet. 21:548-551.
6. de Jong-Gubbels P, van Dijken JP, Pronk JT. 1996. Metabolic fluxes in chemostat cultures of Schizosaccharomyces pombe grown on mixtures of glucose and ethanol. Microbiology. 142:1399-1407.
7. Dietrich FS, Voegeli S, Brachat S, et al. (14 co-authors). 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 304:304-307.
8. Dujon B, Sherman D, Fischer G, et al. (67 co-authors). 2004. Genome evolution in yeasts. Nature. 430:35-44.
9. Fekete V, Cierna M, Poláková S, Piskur J, Sulo P. 2007. Transition of the ability to generate petites in the Saccharomyces/ Kluyveromyces complex. FEMS Yeast Res. 7:1237-1247.
10. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics. 151:1531-1545.
11. Guan Y, Dunham MJ, Troyanskaya OG. 2007. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics. 175:933-943.
12. He X, Zhang J. 2005. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics. 169:1157-1164.
13. Hughes AL. 1994. The evolution of functionally novel proteins after gene duplication. Proc R Soc Lond B Biol Sci. 256:119-124.
14. Kellis M, Birren BW, Lander ES. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 428:617-624.
15. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. 2002. Selection in the evolution of gene duplications. Genome Biol. 3:research0008.1-0008.9.
16. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science. 290:1151-1155.
17. Merico A, Sulo P, Piskur J, Compagno C. 2007. Fermentative lifestyle in yeasts belonging to the Saccharomyces complex. FEBS J. 274:976-989.
18. Ohno S. 1970. Evolution by gene duplication. New York: Springer Verlag.
19. Piskur J. 2001. Origin of the duplicated regions in the yeast genomes. Trends Genet. 17:302-303.
20. Piskur J, Rozpedowska E, Polakova S, Merico A, Compagno C. 2006. How did Saccharomyces yeasts evolve to become a good brewer? Trends Genet. 22:183-186.
21. Satroutdinov AD, Kuriyama H, Kobayashi H. 1992. Oscillatory metabolism of Saccharomyces cerevisiae in continuous culture. FEMS Microbiol Lett. 98:261-267.
22. Scannell DR, Frank A, Conant GC, Byrne KP, Woolfit M, Wolfe KH. 2007. Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc Natl Acad Sci USA. 104:8397-8402.
23. Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP, Benner SA. 2005. Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet. 37:630-635.
24. Tu BP, Kudlicki A, Rowicka M, McKnight SL. 2005. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science. 310:1152-1158.
25. Withers M, Wernisch L, dos Reis M. 2006. Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA. 12:933-942.
26. Wolfe K. 2004. Evolutionary genomics: yeasts accelerate beyond BLAST. Curr Biol. 14:R392-R394.
27. Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 387:708-713.
28. Wood V, Rutherford AI, Ivens A, Rajandream M-A, Barrell B. 2001. A reannotation of the Saccharomyces cerevisiae genome. Comp Funct Genomics. 2:143-154.
29. Zhang J. 2003. Evolution by gene duplication: an update. Trends Ecol Evol. 18:292-298.